"I do trust them, but I think it's a moment when we need to look each other in the eye and decide, are we real allies? Are we going to work together?" Boehner, the top Republican in the US Congress, told NBC television.
"And if we are, you're either all in or you're not in," said the lawmaker, who echoed concerns about how the Al-Qaeda leaders was able to live unperturbed for years just a stone's throw from a top Pakistani military academy.
"Clearly there are questions that remain about what they knew or didn't know about bin Laden being in their country. There are certainly some questions about their willingness to pursue some terrorists, but maybe not others," he said.
Still, Boehner said that when he looks at Pakistan "I see an ally" of the United States and called Islamabad "a real asset when it comes to fighting the war on terror."
"Let's never forget that Pakistan has lost more troops and more individuals than we have here in America. So they've been an ally. They've been helpful. But there are questions, and I don't think we ought to have questions," he said.
"If we're going to really be allies and we're going to fight this war together, we need to be in it together all the time," said the speaker, who is second in line for the presidency after Vice President Joe Biden.
Boehner recently returned from a trip to Afghanistan and Pakistan.